title: Statistical-mechanical lattice models for protein-DNA binding in chromatin.
abstract: Statistical-mechanical lattice models for protein-DNA binding are well established as a method to describe complex ligand binding equilibria measured in vitro with purified DNA and protein components. Recently, a new field of applications has opened up for this approach since it has become possible to experimentally quantify genome-wide protein occupancies in relation to the DNA sequence. In particular, the organization of the eukaryotic genome by histone proteins into a nucleoprotein complex termed chromatin has been recognized as a key parameter that controls the access of transcription factors to the DNA sequence. New approaches have to be developed to derive statistical-mechanical lattice descriptions of chromatin-associated protein-DNA interactions. Here, we present the theoretical framework for lattice models of histone-DNA interactions in chromatin and investigate the (competitive) DNA binding of other chromosomal proteins and transcription factors. The results have a number of applications for quantitative models for the regulation of gene expression.
authors.affiliation: Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum and BioQuant, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany. Vladimir.Teif@bioquant.uni-heidelberg.de
authors.forename: Vladimir B
authors.initials: VB
authors.lastname: Teif
authors.forename: Karsten
authors.initials: K
authors.lastname: Rippe
mesh_terms: D000255:Adenosine Triphosphate / Q000378:metabolism; D001696:Biomechanical Phenomena; D002843:Chromatin / Q000737:chemistry / Q000378:metabolism*; D042002:Chromatin Assembly and Disassembly; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D005786:Gene Expression Regulation; D006657:Histones / Q000737:chemistry / Q000378:metabolism; D055595:Mechanical Phenomena; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009707:Nucleosomes / Q000378:metabolism; D011485:Protein Binding; D055503:Protein Multimerization; D020836:Protein Structure, Quaternary; D013816:Thermodynamics; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D002843:Chromatin; D006657:Histones; D009707:Nucleosomes; D014157:Transcription Factors; D000255:Adenosine Triphosphate; D004247:DNA